You have to find a way to get them in a T-Pose ingame, and rip that. It's usually just a matter of luck. When I ripped the SWAT 4 officers and compiled them as CSS Counter-Terrorists, it was a bit easier than normal because SWAT 4 came with a model viewer in its map editor which you could rip models from in a T-Pose. In the case of Hitman: Blood Money, using the teleport cheat around the mission right after it starts will put every onscreen character into a T-Pose, which you can then rip. Sometimes you can screw up a game's animation files before launching it so that the characters move in T-Poses. (If you're going to do that, make sure you back up everything first...)

Keep in mind that it's always a better idea to extract models directly from the game's files instead of ripping just the mesh when the game is running. You don't risk losing important data, and your output is less likely to be screwed up.

If you can't find a way to get the characters into a T-Pose, and you can't take any data from the game's files, just rip characters in an idle pose. It's messy and more difficult to fix later, but it's really the best you can do.

In all cases, the T-Pose that you rip will be slightly different than the animation you'd need for the Source skeleton. You'll still need to move/rotate/scale the mesh a bit to line it up perfectly.